Re: [AMBER] Joining two molecules

From: Gustaf Olsson <>
Date: Fri, 28 May 2021 08:44:19 +0000

With some help correcting my input, the graft command worked very well in preparing a “joint” molecular structure by aligning, removing overlapping and “bonding”.

This its a really nice addition to CPPTRAJ, should solve some problems aligning and bonding structures.

Thank you very much for the tip, tool and the help Dan, much appreciated. This takes care of generating separate structures and the joint structure, maintaining information available in the input files.

The remaining problem, for me, is still how to retain the desired parameters from two different FFs when loading this new structure, leaving only the “intersect” with as little manual editing involved as possible.

Best regards
// Gustaf

> On 26 May 2021, at 15:33, Daniel Roe <> wrote:
> Hi,
> On Wed, May 26, 2021 at 5:17 AM Gustaf Olsson <> wrote:
>> bond :1.CB,:1.C2
>> Is :1 the now joined molecule? Otherwise, should I provide the correct residue number :2.X,1.X
> No, the bond masks are "<tgt>,<src>" - i.e. they are specific to the
> molecules *before* you join everything. So in the above case, it means
> "bond atom CB in residue 1 of target to atom C2 in residue 1 of
> source". The code will internally update indices to keep track of what
> is what after atoms are removed. Hopefully this clears it up, let me
> know if not
> -Dan
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Received on Fri May 28 2021 - 02:00:03 PDT
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